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- PDB-8h4j: Crystal Structure of AzoR-FMN-Lyb24 complex -

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Basic information

Entry
Database: PDB / ID: 8h4j
TitleCrystal Structure of AzoR-FMN-Lyb24 complex
ComponentsFMN dependent NADH:quinone oxidoreductase
KeywordsBIOSYNTHETIC PROTEIN / AzoR
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavoprotein-like superfamily
Similarity search - Domain/homology
Chem-1IE / FLAVIN MONONUCLEOTIDE / FMN dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae 30684/NJST258_2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHuang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of AzoR-FMN-Lyb24 complex
Authors: Huang, W.
History
DepositionOct 10, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN dependent NADH:quinone oxidoreductase
B: FMN dependent NADH:quinone oxidoreductase
C: FMN dependent NADH:quinone oxidoreductase
D: FMN dependent NADH:quinone oxidoreductase
E: FMN dependent NADH:quinone oxidoreductase
F: FMN dependent NADH:quinone oxidoreductase
G: FMN dependent NADH:quinone oxidoreductase
H: FMN dependent NADH:quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,30924
Polymers182,2238
Non-polymers6,08616
Water18,2311012
1
A: FMN dependent NADH:quinone oxidoreductase
D: FMN dependent NADH:quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0776
Polymers45,5562
Non-polymers1,5224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-24 kcal/mol
Surface area16860 Å2
MethodPISA
2
B: FMN dependent NADH:quinone oxidoreductase
E: FMN dependent NADH:quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0776
Polymers45,5562
Non-polymers1,5224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-24 kcal/mol
Surface area17060 Å2
MethodPISA
3
C: FMN dependent NADH:quinone oxidoreductase
hetero molecules

H: FMN dependent NADH:quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0776
Polymers45,5562
Non-polymers1,5224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5300 Å2
ΔGint-29 kcal/mol
Surface area16890 Å2
MethodPISA
4
F: FMN dependent NADH:quinone oxidoreductase
G: FMN dependent NADH:quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0776
Polymers45,5562
Non-polymers1,5224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-24 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.040, 160.110, 335.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z

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Components

#1: Protein
FMN dependent NADH:quinone oxidoreductase / Azo-dye reductase / FMN-dependent NADH-azo compound oxidoreductase / FMN-dependent NADH-azoreductase


Mass: 22777.814 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae 30684/NJST258_2 (bacteria)
Gene: azoR, KPNJ2_01278 / Production host: Escherichia coli (E. coli)
References: UniProt: W8UQZ7, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor, FMN-dependent NADH-azoreductase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-1IE / ~{N}-(3-methylsulfanylphenyl)-4~{H}-cyclopenta[b]quinolin-9-amine


Mass: 304.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H16N2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1012 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: magnesium chloride, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 128804 / % possible obs: 99.93 % / Redundancy: 13.3 % / Biso Wilson estimate: 34.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06781 / Rpim(I) all: 0.01936 / Net I/σ(I): 24.27
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.7897 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 12789 / CC1/2: 0.895 / Rpim(I) all: 0.2215 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DXP

6dxp


Resolution: 2→44.06 Å / SU ML: 0.2113 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6531
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 6385 4.96 %
Rwork0.1763 122401 -
obs0.178 128786 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.57 Å2
Refinement stepCycle: LAST / Resolution: 2→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12128 0 454 1012 13594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014612861
X-RAY DIFFRACTIONf_angle_d1.626117533
X-RAY DIFFRACTIONf_chiral_restr0.09171994
X-RAY DIFFRACTIONf_plane_restr0.01012272
X-RAY DIFFRACTIONf_dihedral_angle_d22.94184909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.26582180.22234095X-RAY DIFFRACTION99.98
2.02-2.050.25242070.22093996X-RAY DIFFRACTION100
2.05-2.070.26281980.21814076X-RAY DIFFRACTION99.98
2.07-2.10.27351930.20584058X-RAY DIFFRACTION100
2.1-2.130.24762220.20144032X-RAY DIFFRACTION100
2.13-2.150.26462190.20354071X-RAY DIFFRACTION100
2.15-2.190.25282080.2074060X-RAY DIFFRACTION100
2.19-2.220.24951940.19954046X-RAY DIFFRACTION99.98
2.22-2.250.22862200.19564072X-RAY DIFFRACTION100
2.25-2.290.2472360.19454060X-RAY DIFFRACTION100
2.29-2.330.23611950.18784053X-RAY DIFFRACTION100
2.33-2.370.24562230.18874034X-RAY DIFFRACTION100
2.37-2.420.24222200.18964044X-RAY DIFFRACTION100
2.42-2.470.26542430.19254050X-RAY DIFFRACTION100
2.47-2.520.23562040.1854052X-RAY DIFFRACTION100
2.52-2.580.24172180.18644079X-RAY DIFFRACTION100
2.58-2.640.24012130.20114066X-RAY DIFFRACTION99.98
2.64-2.710.2332320.19164031X-RAY DIFFRACTION99.98
2.71-2.790.22721900.1884115X-RAY DIFFRACTION100
2.79-2.880.27131960.1944093X-RAY DIFFRACTION100
2.88-2.990.24532120.19114105X-RAY DIFFRACTION100
2.99-3.110.21092010.18014067X-RAY DIFFRACTION99.98
3.11-3.250.24811850.18484146X-RAY DIFFRACTION100
3.25-3.420.19341730.18324105X-RAY DIFFRACTION99.98
3.42-3.630.18892310.17314091X-RAY DIFFRACTION99.98
3.63-3.910.1992180.16164099X-RAY DIFFRACTION100
3.91-4.310.19622260.15184109X-RAY DIFFRACTION99.91
4.31-4.930.15732440.14124099X-RAY DIFFRACTION100
4.93-6.210.18052390.16614148X-RAY DIFFRACTION99.98
6.21-44.060.17712070.16294249X-RAY DIFFRACTION98.85

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